Sphingosine-1-phosphate lyase polypeptides, polynucleotides and modulating agents and methods of use therefor

ABSTRACT

Compositions, methods and kits for diagnosing and treating cancer are provided. Therapeutic compositions may comprise agents that modulate the expression or activity of a sphingosine-1-phosphate lyase (SPL). Such compositions may be administered to a mammal afflicted with cancer. Diagnostic methods and kits may employ an agent suitable for detecting alterations in endogenous SPL. Such methods and kits may be used to detect the presence of a cancer or to evaluate the prognosis of a known disease. SPL polypeptides, polynucleotides and antibodies are also provided.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.11/782,458, filed Jul. 24, 2007, now pending; which is a continuation ofU.S. patent application Ser. No. 10/979,085, filed Nov. 1, 2004, nowU.S. Pat. No. 7,262,044; which is a continuation of U.S. patentapplication Ser. No. 10/053,510, filed Jan. 17, 2002, now U.S. Pat. No.6,830,881; which is a continuation-in-part of U.S. patent applicationSer. No. 09/356,643, filed Jul. 19, 1999, now U.S. Pat. No. 6,569,666;which is a continuation-in-part of U.S. patent application Ser. No.08/939,309, filed Sep. 29, 1997, now U.S. Pat. No. 6,423,527, whichapplications are incorporated herein by reference in their entireties.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing associated with this application is provided intext format in lieu of a paper copy, and is hereby incorporated byreference into the specification. The name of the text file containingthe Sequence Listing is 200116_(—)402C6_SEQUENCE_LISTING.txt. The textfile is 95 KB, was created on Dec. 22, 2008, and is being submittedelectronically via EFS-Web, concurrent with the filing of thespecification.

BACKGROUND

1. Technical Field

The present invention relates generally to cancer detection and therapy.The invention is more particularly related to sphingosine-1-phosphatelyase polynucleotides and polypeptides, and to agents that modulate theexpression and/or activity of such polypeptides. Such agents may beused, for example, to diagnose and/or treat cancers such as breast andcolon cancer.

2. Description of the Related Art

Breast cancer is a significant health problem for women in the UnitedStates and throughout the world. Although advances have been made indetection and treatment of the disease, breast cancer remains the mostcommon form of cancer, and the second leading cause of cancer death, inAmerican women. Among African-American women and women between 15 and 54years of age, breast cancer is the leading cause of cancer death. Oneout of every eight women in the United States will develop breastcancer, a risk which has increased 52% during 1950-1990. In 1994, it isestimated that 182,000 new cases of female breast cancer were diagnosed,and 46,000 women died from the disease.

No vaccine or other universally successful method for the prevention ortreatment of breast cancer is currently available. Management of thedisease currently relies on a combination of early diagnosis (throughroutine breast screening procedures) and aggressive treatment, which mayinclude one or more of a variety of treatments such as surgery,radiotherapy, chemotherapy and hormone therapy. The course of treatmentfor a particular breast cancer is often selected based on a variety ofprognostic parameters, including an analysis of specific tumor markers.However, the use of established markers often leads to a result that isdifficult to interpret.

With current therapies, tumor invasiveness and metastasis is a criticaldeterminant in the outcome for breast cancer patients. Although the fiveyear survival for women diagnosed with localized breast cancer is about90%, the five year survival drops to 18% for women whose disease hasmetastasized. Present therapies are inadequate for inhibiting tumorinvasiveness for the large population of women with this severe disease.

Colon cancer is the second most frequently diagnosed malignancy in theUnited States as well as the second most common cause of cancer death.The five-year survival rate for patients with colorectal cancer detectedin an early localized stage is 92%; unfortunately, only 37% ofcolorectal cancer is diagnosed at this stage. The survival rate drops to64% if the cancer is allowed to spread to adjacent organs or lymphnodes, and to 7% in patients with distant metastases.

The prognosis of colon cancer is directly related to the degree ofpenetration of the tumor through the bowel wall and the presence orabsence of nodal involvement, consequently, early detection andtreatment are especially important. Currently, diagnosis is aided by theuse of screening assays for fecal occult blood, sigmoidoscopy,colonoscopy and double contrast barium enemas. Treatment regimens aredetermined by the type and stage of the cancer, and include surgery,radiation therapy and/or chemotherapy. Recurrence following surgery (themost common form of therapy) is a major problem and is often theultimate cause of death. In spite of considerable research intotherapies for the disease, colon cancer remains difficult to diagnoseand treat. In spite of considerable research into therapies for theseand other cancers, colon cancer remains difficult to diagnose and treateffectively. Accordingly, improvements are needed in the treatment,diagnosis and prevention of breast and colon cancer. The presentinvention fulfills this need and further provides other relatedadvantages.

BRIEF SUMMARY

Briefly stated, the present invention provides compositions and methodsfor the diagnosis and therapy of cancer. Within one aspect, the presentinvention provides isolated polynucleotides comprising a sequenceselected from the group consisting of: (a) a sequence shown in SEQ IDNO:15; (b) nucleotide sequences that hybridize to a polynucleotidecomplementary to a sequence shown in SEQ ID NO:15 under moderatelystringent conditions, wherein the nucleotide sequences encodepolypeptides having sphingosine-1-phosphate lyase activity; and (c)nucleotide sequences that encode a polypeptide encoded by a sequenceshown in SEQ ID NO:15.

Within a related aspect, an isolated polynucleotide is provided thatencodes a polypeptide shown in SEQ ID NO:16, or a variant of such apolypeptide that has sphingosine-1-phosphate lyase activity. Recombinantexpression vectors comprising any of the foregoing polynucleotides, andhost cells transformed or transfected with such expression vectors, arealso provided.

Within further aspects, SPL polypeptides are provided. Such polypeptidesmay be encoded by any of the foregoing polynucleotides. Alternatively, apolypeptide may comprise an amino acid sequence shown in SEQ ID NO:16,or a variant thereof, wherein the polypeptide hassphingosine-1-phosphate lyase activity.

Within a further aspect, the present invention provides isolatedpolynucleotides comprising at least 100 nucleotides complementary to asequence shown in SEQ ID NO:15.

Within other aspects, methods are provided for preparing asphingosine-1-phosphate lyase, comprising culturing a host celltransformed or transfected with a polynucleotide as described aboveunder conditions promoting expression of the polynucleotide andrecovering a sphingosine-1-phosphate lyase.

In further aspects, the present invention provides methods foridentifying an agent that modulates sphingosine-1-phosphate lyaseactivity. In one such aspect, the method comprises: (a) contacting acandidate agent with a polypeptide comprising a sequence shown in SEQ IDNO:16, or a variant of such a sequence having sphingosine-1-phosphatelyase activity, wherein the step of contacting is carried out underconditions and for a time sufficient to allow the candidate agent tointeract with the polypeptide; and (b) subsequently measuring theability of the polypeptide to degrade sphingosine-1-phosphate or aderivative thereof, relative to an ability in the absence of candidateagent. The step of contacting may be performed by incubating a cellexpressing the polypeptide with the candidate modulator, and the step ofmeasuring the ability to degrade sphingosine-1-phosphate may beperformed using an in vitro assay and a cellular extract.

The present invention further provides pharmaceutical compositionscomprising an agent that modulates sphingosine-1-phosphate lyaseactivity in combination with a pharmaceutically acceptable carrier. Suchagents preferably increase sphingosine-1-phosphate lyase activity. Suchinhibition may be achieved by increasing expression of an endogenous SPLgene, or by increasing the ability of an endogenous SPL to degradesphingosine-1-phosphate. Within certain preferred embodiments, amodulating agent comprises a polynucleotide or an antibody or anantigen-binding fragment thereof.

Within still further aspects, the present invention provides methods formodulating sphingosine-1-phosphate activity, comprising contacting asphingosine-1-phosphate lyase with an effective amount of an agent thatmodulates sphingosine-1-phosphate lyase activity, wherein the step ofcontacting is performed under conditions and for a time sufficient toallow the agent and the sphingosine-1-phosphate lyase to interact. Tomodulate sphingosine-1-phosphate lyase activity in a cell, a cellexpressing sphingosine-1-phosphate may be contacted with such an agent.

Within related aspects, the present invention provides methods forinhibiting the growth of a cancer cell, comprising contacting a cancercell with an agent that increases sphingosine-1-phosphate lyaseactivity. In a preferred embodiment, the cancer cell is a breast cancercell.

The present invention also provides methods for inhibiting thedevelopment and/or metastasis of a cancer in a mammal, comprisingadministering to a mammal an agent that increasessphingosine-1-phosphate lyase activity. Within certain embodiments, anagent may comprise, or be linked to, a targeting component, such as ananti-tumor antibody or a component that binds to an estrogen receptor.

Within other aspects, methods for diagnosing cancer in a mammal areprovided, comprising detecting an alteration in an endogenoussphingosine-1-phosphate lyase gene in a sample obtained from a mammal,and therefrom diagnosing a cancer in the mammal. In certain embodimentsthe cancer is breast or colon cancer and the sample is a breast tumorbiopsy.

In related aspects, the present invention provides methods forevaluating a cancer prognosis, comprising determining the presence orabsence of an alteration in an endogenous sphingosine-1-phosphate lyasegene in a sample obtained from a mammal afflicted with cancer, andtherefrom determining a prognosis.

The present invention further provides isolated antibodies that bind toa polypeptide having a sequence shown in SEQ ID NO:16. Such antibodiesmay be polyclonal or monoclonal, and may increase the ability of apolypeptide having a sequence shown in SEQ ID NO:16 degradesphingosine-1-phosphate.

In still further aspects, the present invention provides methods fordetecting sphingosine-1-phosphate lyase in a sample, comprising: (a)contacting a sample with an antibody as described above under conditionsand for a time sufficient to allow the antibody to bind tosphingosine-1-phosphate lyase; and (b) detecting in the sample thepresence of sphingosine-1-phosphate lyase bound to the antibody.

Kits for use in the above methods are also provided. A kit for detectingsphingosine-1-phosphate lyase in a sample comprises an antibody asdescribed above and a buffer or detection reagent. A kit for detectingan alteration in a sphingosine-1-phosphate gene in a sample comprises apolynucleotide and a detection reagent.

The present invention further provides for a homozygous null mutantDrosophila melanogaster fly line the genome of which comprises aP-element transposon insertion in the coding region of the sphingosinephosphate lyase (SPL) gene wherein said gene encodes the sequence setforth in SEQ ID NO:16, and wherein said fly line has a flightlessphenotype. In a related embodiment, the homozygous mutant fliesdemonstrate abnormal developmental patterning of thoracic muscles of theT2 segment.

The present invention also provides methods for testing an agent capableof inhibiting the development and/or metastasis of a cancer in a mammal,comprising contacting SPL mutant Drosophila progeny with growth mediumcomprising a test agent suspected of inhibiting mammalian sphingosinekinase, and detecting the restoration of flight ability in the progeny.In a related embodiment, the homozygous mutant flies used in this methoddemonstrate abnormal developmental patterning of thoracic muscles of theT2 segment.

The present invention further provides for methods for determining thepresence of a cancer in a patient, comprising the steps of: (a)obtaining a biological sample from the patient; (b) contacting thebiological sample with at least one oligonucleotide that is at leastpartially complementary to the sequence set forth in SEQ ID NO:7; (c)detecting in the sample an amount of said oligonucleotide thathybridizes to the polynucleotide; and comparing the amount ofoligonucleotide that hybridizes to the polynucleotide to a predeterminedcut-off value, and therefrom determining the presence of the cancer inthe patient.

BRIEF DESCRIPTION OF THE SEQUENCE IDENTIFIERS

SEQ ID NO:1 is the determined cDNA sequence of S. cerevisiae SPL.

SEQ ID NO:2 is the amino acid sequence of S. cerevisiae SPL encoded bythe polynucleotide sequence set forth in SEQ ID NO:1

SEQ ID NO:3 is the determined cDNA sequence of C. elegans SPL.

SEQ ID NO:4 is the amino acid sequence of C. elegans SPL encoded by thepolynucleotide sequence set forth in SEQ ID NO:3.

SEQ ID NO:5 is the determined cDNA sequence of the mouse SPL.

SEQ ID NO:6 is the amino acid sequence of mouse SPL encoded by thepolynucleotide sequence set forth in SEQ ID NO:5.

SEQ ID NO:7 is the determined cDNA sequence of the full-length humanSPL.

SEQ ID NO:8 is the amino acid sequence of human SPL encoded by thepolynucleotide sequence set forth in SEQ ID NO:7.

SEQ ID NO:9 is the determined cDNA sequence of a human SPL with adeletion.

SEQ ID NO:10 is the amino acid sequence of a human SPL with a deletion,encoded by the polynucleotide sequence set forth in SEQ ID NO:9.

SEQ ID NO:11 is the amino acid sequence of C. elegans SPL encoded by thepolynucleotide sequence set forth in SEQ ID NO:12.

SEQ ID NO:12 is the determined cDNA sequence of a C. elegans SPL.

SEQ ID NO:13 is a PCR primer.

SEQ ID NO:14 is a PCR primer.

SEQ ID NO:15 is the determined cDNA sequence encoding the Drosophilamelanogaster SPL.

SEQ ID NO:16 is the amino acid sequence of the Drosophila melanogasterSPL, encoded by the cDNA sequence set forth in SEQ ID NO:15.

SEQ ID NO:17 is the determined cDNA sequence of a human SPL as set forthin Genbank Accession No: AF144638.

SEQ ID NO:18 is the amino acid sequence of a human SPL encoded by thepolynucleotide sequence provided in SEQ ID NO:17.

SEQ ID NO:19 is the amino acid sequence of a first Drosophilamelanogaster SK protein.

SEQ ID NO:20 is the amino acid sequence of a second Drosophilamelanogaster SK protein.

SEQ ID NO:21 is the amino acid sequence of a human SK protein.

DETAILED DESCRIPTION

As noted above, the present invention is generally directed tocompositions and methods for the diagnosis and therapy of cancers suchas breast cancer. The invention is more particularly related tosphingosine-1-phosphate lyase (SPL) polypeptides, which have the abilityto cleave sphingosine-1-phosphate into inactive metabolites, and topolynucleotides encoding such polypeptides. Sphingosine-1-phosphate(S-1-P) is an endogenous sphingolipid metabolite present in mostmammalian cells and in serum. Like other sphingolipid metabolites suchas ceramide and sphingosine, S-1-P participates in specific signaltransduction pathways. The results of S-1-P signaling are diverse anddependent upon the cell type being examined. However, many of theeffects of S-1-P signaling, which include promotion of cellularproliferation, enhancement of migration, inhibition of apoptosis andstimulation of angiogenesis, influence the transformation, growth, drugresistance, vascularity and metastatic capacity of cancer cells. Thegene encoding the enzyme responsible for S-1-P synthesis is sphingosinekinase, SK, and S-1-P degradation is sphingosine phosphate lyase, SPLand S-1-P phosphatase, S-1-PP. Several observations support the notionthat SPL may be a cancer related gene. First, altered expression of SPLin human tumors compared to corresponding normal tissue from the samepatient has been shown. Second, human SPL maps to 10q21, a chromosomalregion frequently deleted in a variety of human cancers. Taken together,these observations raise the possibility that SPL may be potentiallyeffective targets for pharmacological intervention in the treatment ofcancer.

Agents that decrease the expression or activity of endogenous SPLpolypeptides are encompassed by the present invention. Such modulatingagents may be identified using methods described herein and used, forexample, in cancer therapy. It has also been found, within the contextof the present invention, that the detection of alterations in anendogenous SPL sequence can be used to diagnose cancer, and to assessthe prognosis for recovery. The present invention further provides suchdiagnostic methods and kits.

As used herein, the term “polypeptide” encompasses amino acid chains ofany length, including full length endogenous (i.e., native) SPL proteinsand variants of endogenous sequences. “Variants” are polypeptides thatdiffer in sequence from a native SPL only in substitutions, deletionsand/or other modifications, such that the variant retains SPL activity,which may be determined using a representative method described hereinSPL polypeptide variants generally encompassed by the present inventionwill typically exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identity along its length,to an SPL polypeptide sequence set forth herein. Within an SPLpolypeptide variant, amino acid substitutions are preferably made at nomore than 50% of the amino acid residues in the native polypeptide, andmore preferably at no more than 25% of the amino acid residues. Suchsubstitutions are preferably conservative. A conservative substitutionis one in which an amino acid is substituted for another amino acid thathas similar properties, such that one skilled in the art of peptidechemistry would expect the secondary structure and hydropathic nature ofthe polypeptide to be substantially unchanged. In general, the followingamino acids represent conservative changes: (1) ala, pro, gly, glu, asp,gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala,phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. Substitutions,deletions and/or amino acid additions may be made at any location(s) inthe polypeptide, provided that the modification does not diminish theSPL activity of the variant. Thus, a variant may comprise only a portionof a native SPL sequence. In addition, or alternatively, variants maycontain additional amino acid sequences (such as, for example, linkers,tags and/or ligands), preferably at the amino and/or carboxy termini.Such sequences may be used, for example, to facilitate purification,detection or cellular uptake of the polypeptide.

When comparing polypeptide sequences, two sequences are said to be“identical” if the sequence of amino acids in the two sequences is thesame when aligned for maximum correspondence, as described below.Comparisons between two sequences are typically performed by comparingthe sequences over a comparison window to identify and compare localregions of sequence similarity. A “comparison window” as used herein,refers to a segment of at least about 20 contiguous positions, usually30 to about 75, 40 to about 50, in which a sequence may be compared to areference sequence of the same number of contiguous positions after thetwo sequences are optimally aligned.

Optimal alignment of sequences for comparison may be conducted using theMegalign program in the Lasergene suite of bioinformatics software(DNASTAR, Inc., Madison, Wis.), using default parameters. This programembodies several alignment schemes described in the followingreferences: Dayhoff, M. O. (1978) A model of evolutionary change inproteins—Matrices for detecting distant relationships. In Dayhoff, M. O.(ed.) Atlas of Protein Sequence and Structure, National BiomedicalResearch Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; HeinJ. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.;Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E. W.and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971) Comb. Theor11:105; Saitou, N. Nei, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P.H. A. and Sokal, R. R. (1973) Numerical Taxonomy—the Principles andPractice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.;Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA80:726-730.

Alternatively, optimal alignment of sequences for comparison may beconducted by the local identity algorithm of Smith and Waterman (1981)Add. APL. Math 2:482, by the identity alignment algorithm of Needlemanand Wunsch (1970) J. Mol. Biol. 48:443, by the search for similaritymethods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT,BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package,Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or byinspection.

One preferred example of algorithms that are suitable for determiningpercent sequence identity and sequence similarity are the BLAST andBLAST 2.0 algorithms, which are described in Altschul et al. (1977)Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol.215:403-410, respectively. BLAST and BLAST 2.0 can be used, for examplewith the parameters described herein, to determine percent sequenceidentity for the polynucleotides and polypeptides of the invention.Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information. For amino acid sequences,a scoring matrix can be used to calculate the cumulative score.Extension of the word hits in each direction are halted when: thecumulative alignment score falls off by the quantity X from its maximumachieved value; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, Tand X determine the sensitivity and speed of the alignment.

The SPL activity of an SPL polypeptide or variant thereof may generallybe assessed using an in vitro assay that detects the degradation oflabeled substrate (i.e., sphingosine-1-phosphate, or a derivativethereof). Within such assays, pyridoxal 5′-phosphate is a requirementfor SPL activity. In addition, the reaction generally proceeds optimallyat pH 7.4-7.6 and requires chelators due to sensitivity toward heavymetal ions. The substrate should be a D-erythro isomer, but inderivatives of sphingosine-1-phosphate the type and chain length ofsphingoid base may vary. In general, an assay as described by VanVeldhoven and Mannaerts, J. Biol. Chem. 266:12502-07, 1991 may beemployed. Briefly, a solution (e.g., a cellular extract) containing thepolypeptide may be incubated with 40 μM substrate at 37° C. for 1 hourin the presence of, for example, 50 mM sucrose, 100 mM K-phosphatebuffer pH 7.4, 25 mM NaF, 0.1% (w/v) Triton X-100, 0.5 mM EDTA, 2 mMDTT, 0.25 mM pyridoxal phosphate. Reactions may then be terminated andanalyzed by thin-layer chromatography to detect the formation of labeledfatty aldehydes and further metabolites. In general, a polypeptide hasSPL activity if, within such an assay: (1) the presence of 2-50 μgpolypeptide (or 0.1-10 mg/mL) results in a statistically significantincrease in the level of substrate degradation, preferably a two-foldincrease, relative to the level observed in the absence of polypeptide;and (2) the increase in the level of substrate degradation is pyridoxal5′-phosphate dependent.

Within certain embodiments, an in vitro assay for SPL activity may beperformed using cellular extracts prepared from cells that express thepolypeptide of interest. Preferably, in the absence of a gene encodingan SPL polypeptide, such cells do not produce a significant amount ofendogenous SPL (i.e., a cellular extract should not contain a detectableincrease in the level of SPL, as compared to buffer alone withoutextract). It has been found, within the context of the presentinvention, that yeast cells containing deletion of the SPL gene (BST1)are suitable for use in evaluating the SPL activity of a polypeptide.bst1Δ cells can be generated from S. cerevisiae using standardtechniques, such as PCR, as described herein. A polypeptide to be testedfor SPL activity may then be expressed in bst1Δ cells, and the level ofSPL activity in an extract containing the polypeptide may be compared tothat of an extract prepared from cells that do not express thepolypeptide. For such a test, a polypeptide is preferably expressed on ahigh-copy yeast vector (such as pYES2, which is available fromInvitrogen) yielding more than 20 copies of the gene per cell. Ingeneral, a polypeptide has SPL activity if, when expressed using such avector in a bst1Δ cell, a cellular extract results in a two-foldincrease in substrate degradation over the level observed for an extractprepared from cells not expressing the polypeptide.

A further test for SPL activity may be based upon functionalcomplementation in the bst1Δ strain. It has been found, within thecontext of the present invention, that bst1Δ cells are highly sensitiveto D-erythro-sphingosine. In particular, concentrations as low as 10 μMsphingosine completely inhibit the growth of bst1Δ cells. Such a levelof sphingosine has no effect on the growth of wildtype cells. Apolypeptide having SPL activity as provided above significantlydiminishes (i.e., by at least two fold) the sphingosine sensitivity whenexpressed on a high-copy yeast vector yielding more than 20 copies ofthe gene per cell.

In general, SPL polypeptides, and polynucleotides encoding suchpolypeptides, may be prepared using any of a variety of techniques thatare well known in the art. For example, a DNA sequence encoding nativeSPL may be prepared by amplification from a suitable cDNA or genomiclibrary using, for example, polymerase chain reaction (PCR) orhybridization techniques. Libraries may generally be prepared andscreened using methods well known to those of ordinary skill in the art,such as those described in Sambrook et al., Molecular Cloning: ALaboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor,N.Y., 1989. cDNA libraries may be prepared from any of a variety ofsources known to contain enzymes having SPL activity. SPL activity isubiquitous with regard to species and mammalian tissues, with theexception of platelets, in which SPL activity is notably absent. In rattissues, the highest levels of activity have been demonstrated inintestinal mucosa, liver and Harderian gland, with low activity inskeletal muscle and heart. Activity has also been demonstrated in anumber of human (hepatoma cell line HB 8065, cervical carcinoma HeLa),mouse (hepatoma line BW1, mouse embryo 3T3-L1, Swiss 3T3 cells) andother cell lines, as well as in human cultured fibroblasts. PreferredcDNA libraries may prepared from human liver, intestine or brain tissuesor cells. Other libraries that may be employed will be apparent to thoseof ordinary skill in the art. Primers for use in amplification may bereadily designed based on the sequence of a native SPL polypeptide orpolynucleotide, as provided herein.

Alternatively, an endogenous SPL gene may be identified using a screenfor cDNAs that complement the BST1 deletion in yeast. A cDNA expressionlibrary may be generated using a regulatable yeast expression vector(e.g., pYES, which is available from Invitrogen, Inc.) and standardtechniques. A yeast bst1Δ strain may then be transformed with the cDNAlibrary, and endogenous cDNAs having the ability to functionallycomplement the yeast lyase defect (i.e., restore the ability to grow inthe presence of D-erythro-sphingosine) may be isolated.

An endogenous SPL gene may also be identified based on cross-reactivityof the protein product with anti-SPL antibodies, which may be preparedas described herein. Such screens may generally be performed usingstandard techniques (see Huynh et al., “Construction and Screening cDNALibraries in λgt11,” in D. M. Glover, ed., DNA Cloning: A PracticalApproach, 1:49-78, 1984 (IRL Press, Oxford)).

Polynucleotides encompassed by the present invention include DNA and RNAmolecules that comprise an endogenous SPL gene sequence. Suchpolynucleotides include those that comprise a sequence recited in anyone of SEQ ID NOs:1-16. Also encompassed are other polynucleotides thatencode an SPL amino acid sequence encoded by such polynucleotides, aswell as polynucleotides that encode variants of a native SPL sequencethat retain SPL activity. Polynucleotides that are substantiallyhomologous to a sequence complementary to an endogenous SPL gene arealso within the scope of the present invention. “Substantial homology,”as used herein refers to polynucleotides that are capable of hybridizingunder moderately stringent conditions to a polynucleotide complementaryto an SPL polynucleotide sequence provided herein, provided that theencoded SPL polypeptide variant retains SPL activity. Suitablemoderately stringent conditions include prewashing in a solution of5×SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50-65° C., 5×SSC,overnight; followed by washing twice at 65° C. for 20 minutes with eachof 2×, 0.5× and 0.2×SSC containing 0.1% SDS. Nucleotide sequences that,because of code degeneracy, encode a polypeptide encoded by any of theabove sequences are also encompassed by the present invention.

Polypeptides of the present invention may be prepared by expression ofrecombinant DNA encoding the polypeptide in cultured host cells.Preferably, the host cells are bacteria, yeast, insect or mammaliancells, and more preferably the host cells are S. cerevisiae bst1Δ cells.The recombinant DNA may be cloned into any expression vector suitablefor use within the host cell and transfected into the host cell usingtechniques well known to those of ordinary skill in the art. A suitableexpression vector contains a promoter sequence that is active in thehost cell. A tissue-specific or conditionally active promoter may alsobe used. Preferred promoters express the polypeptide at high levels.

Optionally, the construct may contain an enhancer, a transcriptionterminator, a poly(A) signal sequence, a bacterial or mammalian originof replication and/or a selectable marker, all of which are well knownin the art. Enhancer sequences may be included as part of the promoterregion or separately. Transcription terminators are sequences that stopRNA polymerase-mediated transcription. The poly(A) signal may becontained within the termination sequence or incorporated separately. Aselectable marker includes any gene that confers a phenotype on the hostcell that allows transformed cells to be identified. Such markers mayconfer a growth advantage under specified conditions. Suitableselectable markers for bacteria are well known and include resistancegenes for ampicillin, kanamycin and tetracycline. Suitable selectablemarkers for mammalian cells include hygromycin, neomycin, genes thatcomplement a deficiency in the host (e.g., thymidine kinase andTK-cells) and others well known in the art. For yeast cells, onesuitable selectable marker is URA3, which confers the ability to grow onmedium without uracil.

DNA sequences expressed in this manner may encode a native SPLpolypeptide (e.g., human), or may encode portions or other variants ofnative SPL polypeptide. DNA molecules encoding variants of a native SPLmay generally be prepared using standard mutagenesis techniques, such asoligonucleotide-directed site-specific mutagenesis, and sections of theDNA sequence may be removed to permit preparation of truncatedpolypeptides.

To generate cells that express a polynucleotide encoding an SPLpolypeptide, cells may be transfected, transformed or transduced usingany of a variety of techniques known in the art. Any number oftransfection, transformation, and transduction protocols known to thosein the art may be used, for example those outlined in Current Protocolsin Molecular Biology, John Wiley & Sons, New York. N.Y., or in numerouskits available commercially (e.g., Invitrogen Life Technologies,Carlsbad, Calif.). Such techniques may result in stable transformants ormay be transient. One suitable transfection technique iselectroporation, which may be performed on a variety of cell types,including mammalian cells, yeast cells and bacteria, using commerciallyavailable equipment. Optimal conditions for electroporation (includingvoltage, resistance and pulse length) are experimentally determined forthe particular host cell type, and general guidelines for optimizingelectroporation may be obtained from manufacturers. Other suitablemethods for transfection will depend upon the type of cell used (e.g.,the lithium acetate method for yeast), and will be apparent to those ofordinary skill in the art. Following transfection, cells may bemaintained in conditions that promote expression of the polynucleotidewithin the cell. Appropriate conditions depend upon the expressionsystem and cell type, and will be apparent to those skilled in the art.

SPL polypeptides may be expressed in transfected cells by culturing thecell under conditions promoting expression of the transfectedpolynucleotide. Appropriate conditions will depend on the specific hostcell and expression vector employed, and will be readily apparent tothose of ordinary skill in the art. For commercially availableexpression vectors, the polypeptide may generally be expressed accordingto the manufacturer's instructions. For certain purposes, expressedpolypeptides of this invention may be isolated in substantially pureform. Preferably, the polypeptides are isolated to a purity of at least80% by weight, more preferably to a purity of at least 95% by weight,and most preferably to a purity of at least 99% by weight. In general,such purification may be achieved using, for example, the standardtechniques of ammonium sulfate fractionation, SDS-PAGE electrophoresis,and/or affinity chromatography.

The present invention further provides antibodies that bind to an SPLpolypeptide. Antibodies may function as modulating agents (as discussedfurther below) to inhibit or block SPL activity in vivo. Alternatively,or in addition, antibodies may be used within screens for endogenous SPLpolypeptides or modulating agents, for purification of SPL polypeptides,for assaying the level of SPL within a sample and/or for studies of SPLexpression. Such antibodies may be polyclonal or monoclonal, and aregenerally specific for one or more SPL polypeptides and/or one or morevariants thereof. Within certain preferred embodiments, antibodies arepolyclonal.

Antibodies may be prepared by any of a variety of techniques known tothose of ordinary skill in the art (see, e.g., Harlow and Lane,Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988).In one such technique, an immunogen comprising an SPL polypeptide orantigenic portion thereof is initially injected into a suitable animal(e.g., mice, rats, rabbits, sheep and goats), preferably according to apredetermined schedule incorporating one or more booster immunizations.The use of rabbits is preferred. To increase immunogenicity, animmunogen may be linked to, for example, glutaraldehyde or keyholelimpet hemocyanin (KLH). Following injection, the animals are bledperiodically to obtain post-immune serum containing polyclonal anti-SPLantibodies. Polyclonal antibodies may then be purified from suchantisera by, for example, affinity chromatography using an SPLpolypeptide or antigenic portion thereof coupled to a suitable solidsupport. Such polyclonal antibodies may be used directly for screeningpurposes and for Western blots.

More specifically, an adult rabbit (e.g., NZW) may be immunized with 10μg purified (e.g., using a nickel-column) SPL polypeptide emulsified incomplete Freund's adjuvant (1:1 v/v) in a volume of 1 mL. Immunizationmay be achieved via injection in at least six different subcutaneoussites. For subsequent immunizations, 5 μg of an SPL polypeptide may beemulsified in complete Freund's adjuvant and injected in the samemanner. Immunizations may continue until a suitable serum antibody titeris achieved (typically a total of about three immunizations). The rabbitmay be bled immediately before immunization to obtain pre-immune serum,and then 7-10 days following each immunization.

For certain embodiments, monoclonal antibodies may be desired.Monoclonal antibodies may be prepared, for example, using the techniqueof Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, andimprovements thereto. Briefly, these methods involve the preparation ofimmortal cell lines capable of producing antibodies having the desiredspecificity (i.e., reactivity with the polypeptide of interest). Suchcell lines may be produced, for example, from spleen cells obtained froman animal immunized as described above. The spleen cells are thenimmortalized by, for example, fusion with a myeloma cell fusion partner,preferably one that is syngeneic with the immunized animal. For example,the spleen cells and myeloma cells may be combined with a nonionicdetergent for a few minutes and then plated at low density on aselective medium that supports the growth of hybrid cells, but notmyeloma cells. A preferred selection technique uses HAT (hypoxanthine,aminopterin, thymidine) selection. After a sufficient time, usuallyabout 1 to 2 weeks, colonies of hybrids are observed. Single coloniesare selected and tested for binding activity against the polypeptide.Hybridomas having high reactivity and specificity are preferred.

Monoclonal antibodies may be isolated from the supernatants of growinghybridoma colonies. In addition, various techniques may be employed toenhance the yield, such as injection of the hybridoma cell line into theperitoneal cavity of a suitable vertebrate host, such as a mouse.Monoclonal antibodies may then be harvested from the ascites fluid orthe blood. Contaminants may be removed from the antibodies byconventional techniques, such as chromatography, gel filtration,precipitation, and extraction.

As noted above, the present invention provides agents that modulate,preferably inhibit, the expression (transcription or translation),stability and/or activity of an SPL polypeptide. To identify such amodulating agent, any of a variety of screens may be performed.Candidate modulating agents may be obtained using well known techniquesfrom a variety of sources, such as plants, fungi or libraries ofchemicals, small molecules or random peptides. Antibodies that bind toan SPL polypeptide, and anti-sense polynucleotides that hybridize to apolynucleotides that encodes an SPL, may be candidate modulating agents.Preferably, a modulating agent has a minimum of side effects and isnon-toxic. For some applications, agents that can penetrate cells arepreferred.

Screens for modulating agents that decrease SPL expression or stabilitymay be readily performed using well known techniques that detect thelevel of SPL protein or mRNA. Suitable assays include RNAse protectionassays, in situ hybridization, ELISAs, Northern blots and Western blots.Such assays may generally be performed using standard methods (seeSambrook et al., Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratories, Cold Spring Harbor, N.Y., 1989). For example, todetect mRNA encoding SPL, a nucleic acid probe complementary to all or aportion of the SPL gene sequence may be employed in a Northern blotanalysis of mRNA prepared from suitable cells. Alternatively, realt-timePCR can also be used to detect levels of mRNA encoding SPL (see Gibsonet al., Genome Research 6:995-1001, 1996; Heid et al., Genome Research6:986-994, 1996). The first-strand cDNA to be used in the quantitativereal-time PCR is synthesized from 20 μg of total RNA that is firsttreated with DNase I (e.g., Amplification Grade, Gibco BRL LifeTechnology, Gaithersburg, Md.), using Superscript Reverse Transcriptase(RT) (e.g., Gibco BRL Life Technology, Gaithersburg, Md.). Real-time PCRis performed, for example, with a GeneAmp™ 5700 sequence detectionsystem (PE Biosystems, Foster City, Calif.). The 5700 system uses SYBR™green, a fluorescent dye that only intercalates into double strandedDNA, and a set of gene-specific forward and reverse primers. Theincrease in fluorescence is monitored during the whole amplificationprocess. The optimal concentration of primers is determined using acheckerboard. The PCR reaction is performed in 25 μl volumes thatinclude 2.5 μl of SYBR green buffer, 2 μl of cDNA template and 2.5 μleach of the forward and reverse primers for the SPL gene, or other geneof interest. The cDNAs used for RT reactions are diluted approximately1:10 for each gene of interest and 1:100 for the β-actin control. Inorder to quantitate the amount of specific cDNA (and hence initial mRNA)in the sample, a standard curve is generated for each run using theplasmid DNA containing the gene of interest. Standard curves aregenerated using the Ct values determined in the real-time PCR which arerelated to the initial cDNA concentration used in the assay. Standarddilution ranging from 20−2×10⁶ copies of the SPL gene or other gene ofinterest are used for this purpose. In addition, a standard curve isgenerated for β-actin ranging from 200 fg-2000 fg. This enablesstandardization of the initial RNA content of a sample to the amount ofβ-actin for comparison purposes. The mean copy number for each sampletested is normalized to a constant amount of β-actin, allowing theevaluation of the observed expression levels of SPL or other gene ofinterest.

To detect SPL protein, a reagent that binds to the protein (typically anantibody, as described herein) may be employed within an ELISA orWestern assay. Following binding, a reporter group suitable for director indirect detection of the reagent is employed (i.e., the reportergroup may be covalently bound to the reagent or may be bound to a secondmolecule, such as Protein A, Protein G, immunoglobulin or lectin, whichis itself capable of binding to the reagent). Suitable reporter groupsinclude, but are not limited to, enzymes (e.g., horseradish peroxidase),substrates, cofactors, inhibitors, dyes, radionuclides, luminescentgroups, fluorescent groups and biotin. Such reporter groups may be usedto directly or indirectly detect binding of the reagent to a samplecomponent using standard methods known to those of ordinary skill in theart.

To use such assays for identifying a modulating agent, the level of SPLprotein or mRNA may be evaluated in cells treated with one or morecandidate modulating agents. An increase or decrease in SPL levels maybe measured by evaluating the level of SPL mRNA and/or protein in thepresence and absence of candidate modulating agent. For example, anantisense modulating agent may be evaluated by assaying the effect onSPL levels. Suitable cells for use in such assays include the breastcancer cell lines MCF-7 (ATCC Accession Number HTB-22) and MDA-MB-231(ATCC Accession Number HTB-26). A candidate modulator may be tested bytransfecting the cells with a polynucleotide encoding the candidate andevaluating the effect of expression of the polynucleotide on SPL levels.Alternatively, the cells may be contacted with a candidate modulator,typically in an amount ranging from about 10 nM to about 10 mM. Acandidate that results in a statistically significant change in thelevel of SPL mRNA and/or protein is a modulating agent.

Alternatively, or in addition, a candidate modulating agent may betested for the ability to inhibit or increase SPL activity, using an invitro assay as described herein (see Van Veldhoven and Mannaerts, J.Biol. Chem. 266:12502-07, 1991) that detects the degradation of labeledsubstrate (i.e., sphingosine-1-phosphate, or a derivative thereof).Briefly, a solution (e.g., a cellular extract) containing an SPLpolypeptide (e.g., 10 nM to about 10 mM) may be incubated with acandidate modulating agent (typically 1 nM to 10 mM, preferably 10 nM to1 mM) and a substrate (e.g., 40 μM) at 37° C. for 1 hour in the presenceof, for example, 50 mM sucrose, 100 mM K-phosphate buffer pH 7.4, 25 mMNaF, 0.1% (w/v) Triton X-100, 0.5 mM EDTA, 2 mM DTT, 0.25 mM pyridoxalphosphate. Reactions may then be terminated and analyzed by thin-layerchromatography to detect the formation of labeled fatty aldehydes andfurther metabolites. A modulating agent (e.g., an antibody) thatincreases SPL activity results in a statistically significant increasein the degradation of sphingosine-1-phosphate, relative to the level ofdegradation in the absence of modulating agent. Such modulating agentsmay be used to increase SPL activity in a cell culture or a mammal, asdescribed below.

A modulating agent may additionally comprise, or may be associated with,a targeting component that serves to direct the agent to a desiredtissue or cell type. As used herein, a “targeting component” may be anysubstance (such as a compound or cell) that, when linked to a compoundenhances the transport of the compound to a target tissue, therebyincreasing the local concentration of the compound. Targeting componentsinclude antibodies or fragments thereof, receptors, ligands and othermolecules that bind to cells of, or in the vicinity of, the targettissue. Known targeting components include hormones, antibodies againstcell surface antigens, lectins, adhesion molecules, tumor cell surfacebinding ligands, steroids, cholesterol, lymphokines, fibrinolyticenzymes and other drugs and proteins that bind to a desired target site.In particular, anti-tumor antibodies and compounds that bind to anestrogen receptor may serve as targeting components. An antibodyemployed in the present invention may be an intact (whole) molecule, afragment thereof, or a functional equivalent thereof. Examples ofantibody fragments are F(ab′)2, -Fab′, Fab and F[v] fragments, which maybe produced by conventional methods or by genetic or proteinengineering. Linkage may be via any suitable covalent bond usingstandard techniques that are well known in the art. Such linkage isgenerally covalent and may be achieved by, for example, directcondensation or other reactions, or by way of bi- or multi-functionallinkers.

For in vivo use, a modulating agent as described herein is generallyincorporated into a pharmaceutical composition prior to administration.A pharmaceutical composition comprises one or more modulating agents incombination with a physiologically acceptable carrier. To prepare apharmaceutical composition, an effective amount of one or moremodulating agents is mixed with any pharmaceutical carrier(s) known tothose skilled in the art to be suitable for the particular mode ofadministration. A pharmaceutical carrier may be liquid, semi-liquid orsolid. Solutions or suspensions used for parenteral, intradermal,subcutaneous or topical application may include, for example, a sterilediluent (such as water), saline solution, fixed oil, polyethyleneglycol, glycerine, propylene glycol or other synthetic solvent;antimicrobial agents (such as benzyl alcohol and methyl parabens);antioxidants (such as ascorbic acid and sodium bisulfite) and chelatingagents (such as ethylenediaminetetraacetic acid (EDTA)); buffers (suchas acetates, citrates and phosphates). If administered intravenously,suitable carriers include physiological saline or phosphate bufferedsaline (PBS), and solutions containing thickening and solubilizingagents, such as glucose, polyethylene glycol, polypropylene glycol andmixtures thereof. In addition, other pharmaceutically active ingredients(including other anti-cancer agents) and/or suitable excipients such assalts, buffers and stabilizers may, but need not, be present within thecomposition.

A modulating agent may be prepared with carriers that protect it againstrapid elimination from the body, such as time release formulations orcoatings. Such carriers include controlled release formulations, suchas, but not limited to, implants and microencapsulated delivery systems,and biodegradable, biocompatible polymers, such as ethylene vinylacetate, polyanhydrides, polyglycolic acid, polyorthoesters, polylacticacid and others known to those of ordinary skill in the art.

Administration may be achieved by a variety of different routes,including oral, parenteral, nasal, intravenous, intradermal,subcutaneous or topical. Preferred modes of administration depend uponthe nature of the condition to be treated or prevented. An amount that,following administration, inhibits, prevents or delays the progressionand/or metastasis of a cancer is considered effective. Preferably, theamount administered is sufficient to result in regression, as indicatedby 50% mass or by scan dimensions. The precise dosage and duration oftreatment is a function of the disease being treated and may bedetermined empirically using known testing protocols or by testing thecompositions in model systems known in the art and extrapolatingtherefrom. Controlled clinical trials may also be performed. Dosages mayalso vary with the severity of the condition to be alleviated. Apharmaceutical composition is generally formulated and administered toexert a therapeutically useful effect while minimizing undesirable sideeffects. The composition may be administered one time, or may be dividedinto a number of smaller doses to be administered at intervals of time.For any particular subject, specific dosage regimens may be adjustedover time according to the individual need.

As an alternative to direct administration of a modulating agent, apolynucleotide encoding a modulating agent may be administered. Such apolynucleotide may be present in a pharmaceutical composition within anyof a variety of delivery systems known to those of ordinary skill in theart, including nucleic acid, bacterial and viral expression systems, andcolloidal dispersion systems such as liposomes. Appropriate nucleic acidexpression systems contain the necessary DNA sequences for expression inthe patient (such as a suitable promoter and terminating signal, asdescribed above). The DNA may also be “naked,” as described, forexample, in Ulmer et al., Science 259:1745-49, 1993.

Various viral vectors that can be used to introduce a nucleic acidsequence into the targeted patient's cells include, but are not limitedto, vaccinia or other pox virus, herpes virus, retrovirus, oradenovirus. Techniques for incorporating DNA into such vectors are wellknown to those of ordinary skill in the art. Another delivery system forpolynucleotides is a colloidal dispersion system. Colloidal dispersionsystems include macromolecule complexes, nanocapsules, microspheres,beads, and lipid-based systems including oil-in-water emulsions,micelles, mixed micelles, and liposomes. The preparation and use ofliposomes is well known to those of ordinary skill in the art.

Within certain aspects of the present invention, one or more modulatingagents may be used to modulate SPL expression and/or activity in vitro,in a cell or in a mammal. In vitro, an SPL polypeptide may be contactedwith a modulating agent that increases or decreases SPL activity (e.g.,certain antibodies). For use within a cell or a mammal, such modulationmay be achieved by contacting a target cell with an effective amount ofa modulating agent, as described herein. Administration to a mammal maygenerally be achieved as described above.

As noted above, increase of SPL expression and/or activity provides amethod for inhibiting the growth (i.e., proliferation) of a cancer cell,either in culture or in a mammal afflicted with cancer. In vivo, suchincrease may also be used to inhibit cancer development, progressionand/or metastasis. Accordingly, one or more modulating agents asprovided herein may be administered as described above to a mammal inneed of anti-cancer therapy. Patients that may benefit fromadministration of a modulating agent are those afflicted with cancer.Such patients may be identified based on standard criteria that are wellknown in the art. Within preferred embodiments, a patient is afflictedwith breast cancer, as identified based on tissue biopsy and microscopicevaluation, using techniques well known in the art. In particular,patients whose tumor cells contain a tissue-specific deletion and/oralteration within an endogenous SPL gene may benefit from administrationof a modulating agent, as provided herein.

Within other aspects, the present invention provides methods and kitsfor diagnosing cancer and/or identifying individuals with a risk formetastasis that is higher or lower than average. It has been found,within the context of the present invention, that certain human tumorcells contain an altered SPL gene. In particular, certain brain tumorcells contain a deletion of amino acid residues 354 to 433 of the humanSPL sequence set forth in SEQ ID NO:8 (cDNA and amino acid sequence ofthe SPL containing the deletion are set forth in SEQ ID NOs:9 and 10,respectively). Specific alterations present in other tumor cells, suchas breast tumor cells, may be readily identified using standardtechniques, such as PCR. Alterations that may be associated with aparticular tumor include amino acid deletions, insertions, substitutionsand combinations thereof. Methods in which the presence or absence ofsuch an alteration is determined may generally be used to detect cancerand to evaluate the prognosis for a patient known to be afflicted withcancer.

To detect an altered SPL gene, any of a variety of well-known techniquesmay be used including, but not limited to, PCR and hybridizationtechniques. Any sample that may contain cancerous cells may be assayed.In general, suitable samples are tumor biopsies. Within a preferredembodiment, a sample is a breast tumor biopsy.

Kits for diagnosing or evaluating the prognosis of a cancer generallycomprise reagents for use in the particular assay to be employed. Ingeneral, a kit of the present invention comprises one or more containersenclosing elements, such as primers, probes, reagents or buffers, to beused in an assay. For example, a kit may contain one or morepolynucleotide primers or probes comprising at least 15 nucleotidescomplementary to a polynucleotide encoding SPL. In certain embodiments,the primers or probes comprise at least 10, 25, 30, 35, 40, 45, 50, 55,60, 65, 70, 75, 80, 85, 90, 95 or 100 nucleotides, and preferably atleast 150 or 200 nucleotides, complementary to an SPL mRNA or to apolynucleotide encoding SPL. Such probe(s) may be used to detect analtered SPL gene by hybridization. For example, a kit may contain oneprobe that hybridizes to a region of an SPL gene that is not generallyaltered in tumors (a control) and a second probe that hybridizes to aregion commonly deleted in breast cancer. A sample that contains mRNAthat hybridizes to the first probe, and not to the second (usingstandard techniques) contains an altered SPL gene. Suitable controlprobes include probes that hybridize to a portion of the SPL geneoutside of the commonly deleted region encoding amino acid resides 354to 433; suitable probes for an altered region include probes thathybridize to a portion of the SPL gene that encodes amino acid residues354 to 433. Alternatively, a kit may comprise one or more primers forPCR analyses, which may be readily designed based upon the sequencesprovided herein by those of ordinary skill in the art. Optionally, a kitmay further comprise one or more solutions, compounds or detectionreagents for use within an assay as described above.

In a related aspect of the present invention, kits for detecting SPL areprovided. Such kits may be designed for detecting the level of SPL ornucleic acid encoding SPL within a sample, or may detect the level ofSPL activity as described herein. A kit for detecting the level of SPL,or nucleic acid encoding SPL, typically contains a reagent that binds tothe SPL protein, DNA or RNA. To detect nucleic acid encoding SPL, thereagent may be a nucleic acid probe or a PCR primer. To detect SPLprotein, the reagent is typically an antibody. The kit may also containa reporter group suitable for direct or indirect detection of thereagent as described above.

Within further aspects, the present invention provides transgenicmammals in which SPL activity is reduced, compared to a wild-typeanimal. Such animals may contain an alteration, insertion or deletion inan endogenous SPL gene, or may contain DNA encoding a modulating agentthat modulates expression or activity of an SPL gene. In certainaspects, such animals may contain DNA encoding a modulating agent thatincreases expression or activity of an SPL gene. Transgenic animals maybe generated using techniques that are known to those of ordinary skillin the art. For example, a transgenic animal containing an insertion ordeletion in the coding region for the SPL gene may be generated fromembryonic stem cells, using standard techniques. Such stem cells may begenerated by first identifying the full genomic sequence of the geneencoding the SPL, and then creating an insertion or deletion in thecoding region in embryonic stem cells. Alternatively, appropriategenetically altered embryonic stem cells may be identified from a bank.Using the altered stem cells, hybrid animals may be generated with onenormal SPL gene and one marked, abnormal gene. These hybrids may bemated, and homozygous progeny identified.

Transgenic animals may be used for a variety of purposes, which will beapparent to those of ordinary skill in the art. For example, suchanimals may be used to prepare cell lines from different tissues, usingwell known techniques. Such cell lines may be used, for example, toevaluate the effect of the alteration, and to test various candidatemodulators.

The invention further provides Drosophila melanogaster animal modelsthat exhibit a flightless phenotype, where the phenotype results fromthe disruption of an endogenous SPL gene as described in greater detailbelow. By flightless phenotype is meant that the subject non-mammaliananimal models spontaneously develop a reduced number of muscle fiberscomprising the dorsal longitudinal muscles (DLM) and have compensatoryhypertrophy in the remaining fibers. In certain aspects, thenon-mammalian animal model of the present invention may also demonstrateabnormal developmental patterning of thoracic muscles of the T2 segment.In a preferred embodiment, the above phenotypes result in an inabilityto fly. The subject non-mammalian animal models, within a preferredembodiment, demonstrate altered activity of the endogenous SPL. In aparticularly illustrative embodiment, said D. melanogaster animal modelshave decreased activity of endogenous SPL.

Within further aspects, the present invention provides mutant strains ofDrosophila melanogaster. In a preferred embodiment, the strain containsa mutation in the SPL gene. In a further embodiment of the presentinvention the D. melanogaster strain are heterozygous for a P-elementtransposon which sits in the coding region of the gene encoding the SPLprotein set forth in SEQ ID NO:16. In a preferred embodiment, the fliesare homozygous insertional mutants in the coding region of the geneencoding the SPL protein set forth in SEQ ID NO:16. In yet a furtherembodiment of the present invention, the homozygous mutant strain of flyhas a flightless phenotype. In certain embodiments, the mutant flieshave a reduced number of muscle fibers comprising the dorsallongitudinal muscles and have compensatory hypertrophy in the remainingfibers. In certain aspects, the mutant flies of the present inventionmay also demonstrate abnormal developmental patterning of thoracicmuscles of the T2 segment.

Flies heterozygous for a P-element transposon which sits in the codingregion of the SPL gene or genes and disrupts production of SPL proteinsmay be obtained from the Drosophila Genome Project. Homozygousinsertional mutants can be made, using techniques known in the art, bygenetically crossing and evaluating progeny for the presence ofhomozygous insertional mutants (based on presence of rosy eye color,encoded by a recessive marker carried on the P-element). Expression ofthe SPL gene can be evaluated using any number of assays known to theskilled artisan, for example, by Northern blot analysis. To determinethe SPL function of each genotype, +/+, +/− and −/− flies may behomogenized using standard techniques and whole extracts can be assayedfor SPL activity using assays as described herein. The transposon can bemobilized by crossing SPL mutant flies with flies carrying an activelytranscribed transposase gene, which should cause the P-element to beexcised in the chromosomes of both somatic cells and in the germline.Germline transposon loss is heritable and can be identified in progenyby virtue of eye color. Progeny which lost both the transposase gene andthe P-element can then be isolated and the restored SPL allele can behomozygosed.

Mutations in Drosophila melanogaster as described herein whichpermanently block expression of a functional protein can be created inseveral ways, such as with P-element transposon insertions or chemicalor radiation induced mutagenesis. Exemplary strains of mutant flies areavailable through the Drosophila Genome Project, at the University ofCalifornia at Berkeley (Adams, M. et al. 2000. The genome sequence ofDrosophila melanogaster. Science. 287:2185-2195.). Alternatively,insertional mutant of interest may be obtained by using local hopstrategies essentially as described in Tower, J. et al (Tower, J., etal. 1993. Preferential transposition of Drosophila P elements to nearbychromosomal sites. Genetics. 133:347-359.), hereby incorporated byreference in its entirety. Transposons can be mobilized by crossing in atransposase gene, followed by crossing the transposase back out(reintroducing genetic stability). Mutant flies can be identified usingtechniques know to those of skill in the art. For example, mutant fliescan be identified by probing Southern blots prepared from extracts fromflies generated in the screen using the target gene as probe.Subsequently, crosses can be performed to introduce a mutant allele ofinterest, (e.g. SPL) and generate homozygosity at both mutant alleles(e.g. SPL and new transposon integration sites). Mutants can be screenedfor a phenotype of interest, for example the ability to restore flightto an SPL mutant when the mutated allele is homozygous (predicting arecessive phenotype).

In one aspect of the present invention, fly genetic manipulation mayentail mating or “crossing” of flies and selection for or againstprogeny expressing various phenotypic markers. Exemplary techniques forfly genetic manipulation of the present invention are know in the artand are described, for example in, Ashburner, M., and J. Roote. 2000.Laboratory culture of Drosophila. In Drosophila Protocols. W. Sullivan,M. Ashburner, and R. Hawley, editors. Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y. 585-600. Phenotypic markers may be usedto identify the inheritance of chromosomes, engineered transposableelements, or transposase genes used to facilitate their mobilization.Marker mutations affecting eye color, bristle shape, wing morphology andcuticle pigmentation, for example, may be employed in the crosses forthe mutant flies of the present invention. Within one aspect of thepresent invention, it may be desirable to select the individuals whichcontain a collection of markers indicating the desired genotype. Inanother aspect of the present invention, balancer chromosomes may beused to create the ability to identify recessive mutations present inthe heterozygous state. Balancer chromosomes may be employed to preventhomologous recombination during meiotic prophase in females. Thepresence of both dominant and recessive lethal markers allows one todetermine the presence or absence of the balancer chromosomes andsimultaneously to follow the homologous chromosomes, which maythemselves not contain a dominant marker. One particularly illustrativecross of the present invention is to eliminate the P-element insertionin the Drosophila SPL gene and establish phenotypic reversion, asdescribed herein in the Examples.

Selective markers to allow for selection of mutant flies is provided forin the present invention. Exemplary selective markers of the presentinvention may comprise a wild type rosy (ry⁺) allele carried on thetransposon to allow for selection for or against the stable transposon.Introduction of an active transposase is selected for by presence of thedominant marker, Stubble (short bristle phenotype) in the first cross,and is selected against to identify progeny which have lost thetransposase, restoring genetic stability in the second cross. Otherillustrative markers include Curly 0 (CyO) which is lethal when presentin two copies, allowing selection for heterozygotes containing the CyObalancer and another allele of interest originally containing thetransposon (e.g., SPL). By selecting against rosy eye color, progeny inwhich the transposon has been excised from the locus of interest, e.g.,SPL, can be identified. Expansion of this “reverted” allele in thepopulation can be achieved in the third cross, and the desired allelecan be homozygosed in the final cross, to determine whether restorationof the intact allele of interest, for example SPL, is associated with adesired phenotype of interest, such as restoration of flight.

In another aspect of the present invention, transgenic flies can becreated using P-elements to overexpress or misexpress proteins ofinterest, such as SPL. In one embodiment of the invention, GAL4-mediatedectopic gene expression is employed, essentially as described (vanRoessel, P., and A. Brand. 2000. GAL4-mediated ectopic gene expressionin Drosophila. In Drosophila Protocols. W. Sullivan, M. Ashburner, andR. Hawley, editors. Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y. 439-448). The GAL4 protein is a yeast transcription factorcapable of activating transcription of Drosophila genes which have beenengineered to contain upstream sequences recognized by the GAL4 protein.Various mutants can be created with a gene of interest expressed inspecific tissue distributions, a construct containing the gene ofinterest (reporter) under regulation of a GAL4 containing promoter isintroduced into embryos, and a genetic marker allows identification ofprogeny containing this construct. Illustrative GAL4 containingpromoters include, but are not limited to, pUAS. The use of embryos of astrain containing an active P-transposase increases the efficiency oftransgene integration, although many of the embryos die. These progenycan then be crossed to various available lines containing GAL4transgenes (driver) expressed under control of tissue-specificpromoters. In one aspect of the present invention, GAL4 driverconstructs which allow expression during embryogenesis are used.

The following Examples are offered by way of illustration and not by wayof limitation.

EXAMPLES Example 1 Isolation and Characterization of SPL cDNA from Yeast

This Example illustrates the preparation of an S. cerevisiae cDNAmolecule encoding an endogenous SPL polypeptide.

Wild-type yeast cells (SGP3 (Garrett and Broach, Genes and Dev.3:1336-1348, 1989); leu2-3,112 trp1 ura3-52 his3 ade8 ras1::HIS3) weretransformed with a yeast genomic library carried on the pRS202 high-copyshuttle vector (Sikorski and Heiter, Genetics 122:19-27, 1989)containing a selectable nutritional marker (URA3). pRS202 is a modifiedversion of the pRS306 vector, into which a 2 micron plasmid piece wasinserted. Inserts from this library are approximately 6-8 kb in length.Wild type yeast were transformed with the high copy library as describedby Ito et al., J. Bact. 153:163-68, 1983, selected for uracilprototrophy (i.e., the ability to grow on medium lacking uracil), andtransformants were pooled and replated at a concentration of 10⁶ cellsper plate onto 1 mM D-erythro-sphingosine plates.

Six transformants which grew large colonies on 1 mMD-erythro-sphingosine plates were grown in selective medium, and controlSGP3 colonies were grown in minimal medium, at 30° C. until saturated.Absorbance at 660 nm was used to correct for small variations in cellconcentration between cultures. Serial dilutions were performed, andcells were template-inoculated onto 1 mM D-erythro-sphingosine platesand incubated at 30° C. for 48 hours.

The most highly represented insert, 13-1, was subcloned and sequenced,and named BST1 (bestower of sphingosine tolerance; GenBank accessionnumber U51031; Saccharomyces cerevisiae genome database accession numberYDR294C). The BST1 nucleotide sequence encodes a previously unknownpredicted protein of 65,523 kilodaltons and 589 amino acids in length.This sequence is 23% identical to gadA and gadB, two nearly identical E.coli genes encoding glutamate decarboxylase (GAD), apyridoxal-5′-phosphate-dependent enzyme which catalyzes synthesis of theneurotransmitter γ-amino butyric acid. BST1 has been localized to S.cerevisiae chromosome 4. The DNA sequence of BST1 is provided in SEQ IDNO:1, which encodes the amino acid sequence set forth in SEQ ID NO:2.

To explore the function of BST1, a deletion strain was created throughhomologous recombination using a NEO selectable marker (Wach et al.,Yeast 10:1793-1808, 1994). Genomic BST1 was replaced with kanMX (Wach etal., Yeast 10:1793-1808, 1994), which confers resistance to G418.Disruption was confirmed using PCR amplification of genomic DNA fromG418 resistant clones, using primers to genomic sequence just 5′ and 3′to the region replaced by the disruption. Deletion of BST1 and allsubsequent biological studies were performed in both SGP3 and in JK93d(Hietman et al., Proc. Natl. Acad. Sci. USA 88:1948-52, 1991); ura3-52leu2-3,112 his4 trp1 rme1). Heterozygous diploids were sporulated, andspores segregated 2:2 for G418 resistance. Both G418 resistant andsensitive progeny were viable, indicating that BST1 is not an essentialgene.

Analysis of GAD activity in cytosolic extracts from wild type, BST1overexpression and bst1Δ strains indicated that BST1 does not encode theS. cerevisiae homologue of GAD. However, deletion of BST1 was associatedwith severe sensitivity to D-erythro-sphingosine. Concentrations as lowas 10 μM sphingosine completely inhibited growth of bst1Δ strains buthad no effect on the viability of wild type cells. In comparison to thecontrol strain, the bst1Δ strain also demonstrated greater sensitivityto 100 μM phytosphingosine, the long chain base endogenous to S.cerevisiae. No difference between the growth of wild type and BST1overexpression strains on phytosphingosine, which is only minimallytoxic to wild type cells at this concentration, was observed.

To determine whether differences in sphingosine uptake or metabolismwere responsible for these sensitivity differences, BST1 wild type,overexpression and bst1Δ strains were exposed to [C3-³H]labeledsphingosine (American Radiolabeled Chemical, Inc., St. Louis, Mo.),washed in sterile water and subjected to Bligh-Dyer extractions (Blighand Dyer, Can. J. Buichem. Physiol. 37:911-17, 1959). There were nomajor differences in sphingosine recovery among the three strains.However, the aqueous phase from the bst1Δ strain contained a ten-foldincrease in radioactivity over that of control and BST1 overexpressionstrains. Thin layer chromatography (TLC) analysis of the lipid fractionsin butanol:acetic acid:water (3:1:1) revealed a sphingosine band whichappeared equivalent in each strain.

Radioactive sphingosine-1-phosphate (S-1-P) was also observed in theextracts from the bst1Δ strain, but not in the wild type or BST1overexpression strains. This compound accumulated rapidly, reaching aplateau by 60 minutes. Three separate TLC conditions were used toconfirm the presence of S-1-P. These conditions, along with theresulting RF values, are shown below:

butanol:water:acetic acid (3:1:1) .47 chloroform:methanol:water(60:35:8) .22 chloroform:methanol:water:acetic acid (30:30:2:5) .33

Hyperaccumulation of S-1-P and hypersensitivity to D-erythro-sphingosinesuggest a failure to metabolize S-1-P, indicating that BST1 is a yeastSPL. To confirm this identification, lyase activity in BST1 wild type,overexpression and deletion strains were evaluated as described byVeldhoven and Mannaerts, J. Biol. Chem. 266:12502-07, 1991, usingunlabeled D-erythro-dihydrosphingosine-1-phosphate (Biomol, PlymouthMeeting, Pa.) and D-erythro-dihydrosphingosine [4,5-³H] 1-phosphate(American Radiolabeled Chemicals, Inc., St. Louis, Mo.). Specificactivity was 100 mCi/mmol. SPL activity was found to correlate with BST1expression, confirming BST1 to be the yeast homologue ofsphingosine-1-phosphate lyase.

These results indication that BST1 is a yeast SPL, and that SPLcatalyzes a rate-limiting step in sphingolipid catabolism. Regulation ofSPL activity may therefore result in regulation of intracellular S-1-Plevels.

Example 2 Isolation and Characterization of SPL cDNA from C. elegans andMouse

This Example illustrates the identification of endogenous SPL cDNAs fromC. elegans and Mus musculus.

Comparison of the yeast BST1 sequence to sequences within the GenBankdatabase identified a full length gene from C. elegans that wasidentified during the systematic sequencing of the C. elegans genome.This cDNA sequence is set forth in SEQ ID NO:3 and was found to encodeSPL, the sequence set forth in SEQ ID NO:4. This and other DNA homologysearches described herein were performed via the National Center forBiotechnology Information website using BLAST search program.

Using both S. cerevisiae and C. elegans SPL sequences to search the ESTdatabase, an expressed sequence tag from early embryonic cells of themouse (day 8 embryo, strain C57BL/6J) was identified. The cDNA clonecontaining this putative mouse SPL was purchased from Genome Systems,Inc (St. Louis, Mo.). Completion of the full length cDNA sequencerevealed an 1707 bp open reading frame. This mouse sequence showedsignificant homology to BST1 and to other pyridoxal phosphate-bindingenzymes such as glutamate decarboxylase, with greatest conservationsurrounding the predicted pyridoxal phosphate-binding lysine. Since thetwo genes encoding mouse glutamate decarboxylase have been identifiedpreviously, and the identified sequence was unique and had no knownfunction, it was a likely candidate mouse SPL gene.

To confirm the SPL activity of the mouse gene, a two step process wasundertaken. First, the sequence was cloned into the high-copy yeastexpression vector, pYES2 (Invitrogen, Inc., Carlsbad, Calif.), in whichthe gene of interest is placed under control of the yeast GAL promoterand is, therefore, transcriptionally activated by galactose andrepressed by glucose. pYES2 also contains the URA3 gene (which providestransformants the ability to grow in media without uracil) and anampicillin resistance marker and origin of replication functional in E.coli.

The expression vector containing the full-length mouse SPL gene was thenintroduced into the yeast bst1Δ strain which, as noted above, isextremely sensitive to D-erythro-sphingosine, as a result of metabolismof sphingosine to S-1-P. S-1-P cannot be further degraded in the absenceof SPL activity and overaccumulates, causing growth inhibition.Transformation was performed using the lithium acetate method (Ito etal., J. Bact. 153:163-68, 1983). Transformants were grown on mediumcontaining 20 g/L galactose and selected for uracil prototrophy.

Transformants were then evaluated for sphingosine resistance. Strains ofinterest were grown to saturation in liquid culture for 2-3 days. Theywere then resuspended in minimal medium, placed in the first row of a96-well plate and diluted serially from 1:2 to 1:4000 across the plate.The cultures were then template inoculated onto a control plate (YPD)and a plate containing minimal synthetic media supplemented with 50 μMD-erythro-sphingosine (Sigma Chemical Co., St. Louis, Mo.) and 0.0015%NP40 (Sigma Chemical Co.). At this concentration of NP40, no effects oncell viability were observed. Plates were incubated at 30° C. for twodays and assessed visually for differences in growth. Transformantscontaining the mouse SPL gene were resistant to sphingosine present ingalactose-containing plates. A strain transformed with vector aloneremained sensitive to sphingosine. Therefore, the mouse SPL gene wascapable of reversing the sphingosine-sensitive phenotype of a yeastbst1Δ strain.

In order to determine whether the mouse SPL gene was able to restorebiochemical SPL activity to the bst1Δ strain, the untransformed bst1Δstrain, and the bst1Δ strain transformed with pYES2 containing eitherBST1 or the putative mouse SPL gene were grown to exponential phase(A₆₀₀=1.0) in either minimal (JS16) or uracil medium containinggalactose as a carbon source. Whole cell extracts were prepared fromeach strain as described above, adjusted for protein concentration, andevaluated for sphingosine phosphate lyase activity as described above,using ³H-dihydrosphingosine-1-phosphate (American RadiolabeledChemicals, Inc., St. Louis, Mo.). Qualitative analysis of product wasperformed by autoradiography. Quantitative measurement was performed byscraping TLC plates and determining radioactivity present using astandard scintillation counter.

The results of the sphingosine phosphate lyase assays shown thatexpression of both the yeast and mouse sequences restored SPL activityto the bst1Δ strain, whereas vector alone had no effect, confirming theidentity of the mouse sequence as SPL.

To determine whether the expression of the mouse SPL transcriptcoincided with previously reported tissue-specific SPL activity in themouse, total RNA was obtained from a variety of mouse tissues and probedwith the complete mouse SPL cDNA sequence. Northern analysis wasperformed as described by Thomas, Proc. Natl. Acad. Sci. USA 77:5201,1980, using a full length mouse SPL cDNA probe labeled by randomlabeling technique (Cobianchi and Wilson, Meth. Enzymol. 152:94-110,1987). This analysis revealed a pattern of expression consistent withthe known SPL activity in various mouse tissues, providing furtherconfirmation that this sequence encodes mouse SPL.

Example 3 Isolation and Characterization of Human SPL cDNA

This Example illustrates the identification of an endogenous human cDNA.

An EST database was searched using the mouse SPL sequence describedherein. Two distinct EST sequences having strong homology to the mousesequence were identified from human sources. One of these sequencescorresponded to the C-terminus, and the other corresponded to theN-terminus. Primers were designed based on these sequences, and a DNAfragment was amplified by PCR from a human expression library made fromhuman glioblastoma multiforme tissue RNA. The fragment was sequenced andwas shown to contain a deletion, so the primers were used to amplify thegene from human fibroblast RNA. This gene has the sequence provided inSEQ ID NO:7 and encodes the polypeptide sequence provided in SEQ IDNO:8. The cDNA and amino acid sequences of the SPL containing thedeletion are set forth in SEQ ID NOs:9 and 10, respectively.

Example 4 Isolation and Characterization of C. Elegans SPL cDNA

This Example illustrates the identification of a cDNA molecule encodinga primary C. elegans sphingosine phosphate lyase.

The human SPL cDNA sequence was used to screen the ACEdb C. elegansgenome database. A potential C. elegans open reading frame of unknownfunction present on YAC Y66H₁B showed substantial (40%) homology toyeast, human and mouse SPL cDNA sequences. To clone this sequence, acoupled reverse transcriptase/polymerase chain reaction was performedusing the Access RT-PCR system (see below). Template was C. eleganstotal RNA, and primers were:

5′-GAGGAATTCATGGATTCGGTTAAGCACACAACCG-3′5′-AGCCTCGAGTTAATTAGAAGTTGAAGGTGGAGC-3′

This resulted in a DNA fragment cSPL2, which was ligated into the yeastexpression vector pYES2, obtained from Invitrogen. Inc. (Carlsbad,Calif.). Genes expressed using this system are regulated under thecontrol of the GAL promoter, which allows expression in the presence ofgalactose and not in the presence of glucose. The nucleotide sequence ofcSPL2 is set forth in SEQ ID NO:12, with the encoded amino acid sequenceset forth in SEQ ID NO:11

cSPL2 was further analyzed for its ability to complement the sphingosinesensitive phenotype of a yeast dpl1 mutant, the previously describedyeast strain JS16 which contains a large deletion in DPL1, the S.cerevisiae sphingosine phosphate lyase gene (Zhou and Saba, BiochemBiophys Res Commun 242:502-507, 1998). Transformation of JS16 with pYES2or the C. elegans SPL-pYES2 construct was performed by the lithiumacetate method (Ito et al., J. Bact. 153:163-168, 1983). Transformantswere selected for uracil prototrophy and evaluated for sphingosineresistance using the dilutional assay described by Zhou and Saba,Biochem Biophys Res Commun 242:502-507, 1998. Cells were grown inminimal or uracil⁻ media containing either 20 g glucose or galactose perliter, as indicated. D-erythro-sphingosine and NP40 were obtained fromSigma Chemical Company (St. Louis, Mo.).

The results demonstrate that cSPL2 convincingly complemented the yeastmutant, restoring enzyme activity. In each plate, yeast were grown tosaturation in overnight liquid cultures, spun down, resuspended in 200microliters of water and dispensed into the first (left-most) well ofeach horizontal row. Yeast were then further diluted into sterile water,so the second well was 1:2, third well was 1:4, fourth well was 1:40,fifth was 1:400 and sixth was 1:4000 dilution from the original on theleft. The toxicity of sphingosine is cell number dependent, because itdisperses itself in cell membranes. Therefore, the concentration ofsphingosine in the plate is not the only thing affecting toxicity, andthese dilutional assays show differences in tolerance/sensitivity. So, astrain which can grow in the sixth row is about 4,000 times moreresistant to sphingosine than one which can grow only in the first row.

The mutant yeast strain containing cSPL2 also demonstrated substantialSPL activity. The sphingosine phosphate lyase assay used whole cellextracts of yeast containing either pYES2 vector alone or (cSPL2) C.elegans SPL-pYES2. Extracts were prepared as described by Saba et al., JBiol Chem 272:26087, 1997. SPL activity was determined essentially asdescribed, using ³H-dihydrosphingosine-1-phosphate substrate (see Zhouand Saba, Biochem Biophys Res Commun 242:502-507, 1998). Substrate forSPL assay (³H-dihydrosphingosine-1-phosphate) was obtained from AmericanRadiolabeled Chemicals, Inc. (St. Louis, Mo.). Access RT-PCR system wasobtained from Promega Corp. (Madison, Wis.).

Enzyme activity in (cSPL2) C. elegans SPL-pYES2 was appreciably greaterthan that of the vector control. These results indicate that cSPL2encodes the primary C. elegans SPL.

Example 5 Developmental Defects Induced by RNA Interference in C.elegans

In order to determine the effect of blocking cSPL2 expression on thedevelopment of C. elegans, RNA interference studies were undertaken. ThecSPL2 cDNA was cloned into pBluescript such that the insert was flankedby the T3 and T7 promoter regions. RNA complementary to each strand wassynthesized from these promoters using an in vitro transcription kit(Promega, Madison, Wis.). The two strands were annealed to make doublestranded RNA (dsRNA) and injected into the distal gonads of 12 wild-type(N2 Bristol) young adult C. elegans hermaphrodites. As controls,uninjected hermaphrodites as well as hermaphrodites injected with adsRNA that does not produce a visible phenotype were handled inparallel. Eight hours after injection, each hermaphrodite wastransferred to a fresh culture plate and 12 hour cohorts of F1 progenywere established. Progeny were observed daily with a dissectingmicroscope until most animals reached adulthood and the culture platesbecame too crowded with F2 progeny. Compared to control F1s, animalsinheriting cSPL-2 dsRNA developed slowly, moved sluggishly, were thinand pale, and did not pump food actively. These animals reach adulthoodapproximately 24 hours later than controls. Adult hermaphrodites thatinherited cSPL-2 dsRNA were markedly different from controls especiallyin the gonad and uterus. Control animals had abundant nuclei in thedistal gonad and a row of developing oocytes in the proximal gonad.Affected hermaphrodites had poorly developed distal gonads with fewernuclei. Control adults had embryos of progressive stages of developmentin the uterus, whereas the number of developing oocytes in the proximalgonad of affected hermaphrodites was reduced. The embryos in the uterusof affected progeny were also abnormal. Those near the vulva were atlate developmental stages indicating a defect in egg laying. There wasnot a uniform progression of developmental stages in adjacent embryossuggesting a defect in ovulation or development, and some of the embryosshowed abnormal patterns of cell division. In summary, inhibition of C.elegans SPL expression through the use of RNA interference leads to poorfeeding, developmental abnormalities and impaired fertility in theprogeny. These results suggest that SPL is an essential gene in C.elegans.

Example 6 Isolation and Characterization of SPL cDNA from Drosophilamelanogaster

In order to seek out the Drosophila melanogaster SPL cDNA and genomicsequence, the D. melanogaster genomic database was searched forsequences which demonstrated significant homology to human SPL cDNA.This led to identification of two full-length cDNA clones (LP04413 andGH3783) which were confirmed by sequence and restriction analysis. Thetwo clones are predicted based on alternative 5′ exon usage and may beexpressed in different subcellular locations. The predicted Drosophilamelanogaster SPL is located on the right arm of chromosome II, position53F8-12. The cDNA sequence for Drosophila melanogaster SPL is set forthin SEQ ID NO:15 and encodes the SPL protein set forth in SEQ ID NO:16.The Drosophila SPL predicted protein sequence set forth in SEQ ID NO:16is 49%, 49% and 43% identical to human, mouse and yeast SPL proteinsequences, respectively.

In order to evaluate whether these clones contained a functional SPLgene, they were recloned into the yeast expression vector, pYES2, andthis construct was transformed into a dpl1Δ strain. Expression of clonescontaining the potential Drosophila melanogaster SPL fully complementthe dpl1Δ strain's sensitivity to 50 μM D-erythro-sphingosine. Further,whole cell extracts of dpl1 strains containing either pYES2-LP04413 orpYES2-GH3783 demonstrate restoration of SPL enzyme activity to wild typelevels or greater, although not as high as a DPL1 overexpressing strain(DPL OE).

Example 7 Generation and Characterization of SPL transposon mutant D.melanogaster

Flies heterozygous for a P-element transposon which sits in the codingregion of both of the above transcripts described in Example 6 andpresumably disrupts both SPL proteins were obtained from the DrosophilaGenome Project. These flies were genetically crossed using techniqueswell known to ordinarily skilled artisans, and progeny were evaluatedfor the presence of homozygous insertional mutants (based on presence ofrosy eye color, encoded by a recessive marker carried on the P-element).Northern blot analysis from wild type and SPL insertional mutant fliesindicated that no SPL gene expression occurred in the latter.

To determine the SPL function of each genotype, +/+, +/− and −/− flieswere homogenized and whole extracts assayed for SPL activity. It wasobserved that SPL genotype corresponded with SPL activity with+/+>+/−>−/−. Initial evaluation of homozygous mutants indicated thatadult SPL mutants were flightless, suggesting a potential defect ineither muscle development or energetics of the adult fly. Flightanalysis was carried out essentially as described (Vigoreaux, J., J.Saide, K. Valgeirdottir, and M. Pardue. 1993. Flightin, a novelmyofibrillar protein of Drosophila stretch-activated muscles. J CellBiol. 121:587-598) by determining the percentage of flies that wereflightless or exhibited downward, upward, or lateral flight capabilitiesin control Canton-S flies as compared to mutant flies.

The transposon was mobilized by crossing SPL mutant flies with fliescarrying an actively transcribed transposase gene, which caused theP-element to be excised in the chromosomes of both somatic cells and inthe germline. Germline transposon loss is heritable and was identifiedin progeny by virtue of eye color. Progeny which lost both thetransposase gene and the P-element were then isolated and the restoredSPL allele was homozygosed. Progeny which had lost the P-element at theSPL locus demonstrated restoration of flight, indicating that thephenotype correlated with the P-element insertional mutation. Todetermine the etiology of the flightlessness of −/− flies, flies weresectioned through the thoracic region and indirect flight muscles wereevaluated by both light and electron microscopy. These studies revealeda reduced number of muscle fibers comprising the dorsal longitudinalmuscles with evidence of what appears to be compensatory hypertrophy inthe fibers which remained. Electron microscopy revealed noultrastructural defects in the myocytes which remained.

In order to determine whether the loss of SPL expression was due toexcess accumulation of S-1-P in the developing adult fly, we salvagedthe developing flight muscles of homozygous SPL mutant progeny by addingD,L-threo-dihydrosphingosine, an inhibitor of mammalian sphingosinekinase, to the growth media. A significant proportion of homozygous SPLmutant progeny demonstrated restoration of flight when grown on mediasupplemented with D,L-threo-dihydrosphingosine.

Northern analysis was performed to investigate SPL expression throughoutdevelopment. These studies indicated that SPL expression begins at 8-12hours of embryonic development and remains detectible throughout larvalstages and pupation.

Therefore, the Drosophila melanogaster model described herein can beused to identify pharmacologic suppressors of SPL mutant flies'inability to fly. Drugs which alter SPL activity or expression may beeffective treatment for at least some kinds of cancer. Therefore, thefact that a fruitfly SPL null mutant containing a P-element insertionwithin the SPL coding region is flightless provides an excellent modelin which to screen and identify compounds that modulate SPL activity.Thus, other chemicals created through rational drug design approachescan be screened using this method. The Drosophila melanogaster modeldescribed herein can thus be used to screen an array of rationallydesigned chemicals with homology to sphingolipids for their ability torestore flight to SPL mutant progeny. Candidate drugs identified usingthis method can then be further evaluated in an in vitro yeast screen.

Example 8 Further Characterization of Developmental Expression Patternsof SPL in SPL Transposon Mutant D. melanogaster

Northern analysis is carried out and extended to include adult samples,and blots are reprobed with SPL specific probes using the followingapproaches. Once genes are confirmed to encode the predicted enzyme, DNAprobes or riboprobes for SPL and S-1-P phosphatase are labeled eitherradioactively or with digoxygenin. For Northern analysis, full-lengthprobes are labeled by random priming with [α-³²P]dATP. Hybridization iscarried out under standard conditions against an RNA blot prepared fromtotal RNA of flies harvested at different stages of development (embryosat hours 0-4, 4-8, 8-12, 12-24, larval instars 1^(st), 2^(nd), 3^(rd),early and late pupal stages, and adults). For in situ hybridizationpurposes, ³H labeling is the most sensitive approach, and the very lowenergy of the beta particle emitted causes it to travel only shortdistances through the radiographic emulsion, allowing preciselocalization for the probe. However, digoxygenin labeling provides theadvantage of being able to visualize hybridization with much higherspatial resolution because of the ability to directly visualize thetissue. Random primer labeling of DNA are performed with either tritiumor digoxygenin labeled nucleotides. In situ hybridization is performedas described in Blair, S. (Blair S., 2000. Imaginal discs. In DrosophilaProtocols. W. Sullivan, M. Ashburner, and R. Hawley, editors. ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 159-175),hereby incorporated by reference in its entirety.

Example 9 Characterization of Sphingolipid Species in the DrosophilaMelanogaster

Without being bound by theory, it is hypothesized that the phenotype ofthe SPL mutant Drosophila is caused by an abnormal level of S-1-P duringdevelopment. Further, without being bound by theory, it is theinventors' hypothesis that phosphorylated sphingoid base species areresponsible for regulating cell proliferation, migration and otherevents required for both tumor formation and normal developmentalprocesses in this model organism. Therefore, characterization ofsphingolipid species in Drosophila was determined.

Method: Wild type (Canton S) whole fly extracts were prepared bymechanical disruption. Lipids were isolated by two-phase extraction andderivatized with the fluorescent molecule o-pthalaldehyde essentially asdescribed in Caligan, et al. hereby incorporated by reference in itsentirety (Caligan, T. B., K. Peters, J. Ou, E. Wang, J. Saba, and A. H.Merrill, Jr. 2000. A high-performance liquid chromatographic method tomeasure sphingosine 1-phosphate and related compounds from sphingosinekinase assays and other biological samples. Analytical Biochemistry.281:36-44). Derivatized lipid extracts were separated by HPLC using aC₁₈ ODS column (LUNA 4.6×250 mm) and mobile phase MeOH/H₂0/1M TBAP82:17:0.9, pH 4.8. Standards included commercially available C₁₀, C₁₂,C₁₄, C₁₆, C₁₈ and C₂₀ sphingosines, as well as the phosphorylated formsof these standards, prepared by incubation of sphingosine standards withextract from a yeast strain which overexpresses the major yeastsphingosine kinase, LCB4.

Results: Drosophila extracts contained only sphingolipid species whichcomigrated with C₁₄ sphingosine and C₁₄ sphingosine-1-phosphate (S-1-P)standards under the stated conditions. To verify the identity of thepeaks in fly extracts which comigrated with C₁₄sphingosine and C₁₄S-1-Pstandards, extracts and standards were compared in four different mobilephase buffers. The peak identified as C₁₄ sphingosine comigrated withthe C₁₄ sphingosine standard under all four conditions (Table 1).However, the peak identified as C₁₄S-1-P demonstrated a slightdifference from the C₁₄S-1-P standard under conditions which exploitdifferences in charge (MeOH/10 mM KP/1 M TBAP, pH 7.2, 81:18:1).

TABLE 1 Sphingolipid Identification C₁₄S C₁₄S-1-P C₁₄S-1-P Mobile PhaseC₁₄S std in extract std in extract MeOH/H₂0/1M 19.1 min 19.0 min 14.8min 14.8 min TBAP pH 4.8 82.1:17:0.9 MeOH/H₂0/1M 27.3 min 27.1 min 22.5min 22.1 min TBAP pH 4.8 79.1:20:0.9 MeOH/10 mM KP/ 21.9 min 22.0 min18.3 min 17.2 min 1M TBAP pH 5.5 81:18.1 MeOH/10 mM KP/ 21.4 min 21.8min 15.0 min 17.1 min 1M TBAP pH 7.2 81:18.1

This finding is likely to be due to a chemical modification of thephosphate group, since a phosphatase capable of dephosphorylating theC₁₄S-1-P standard does not recognize this substrate. Mass spectroscopyis utilized to identify the phosphate group modification of this S-1-Pspecies. Herein, this sphingolipid is referred to as “modifiedC₁₄S-1-P.”

Example 10 Characterization of Sphingolipid Species in the DrosophilaSPL Mutant

Differences in the quantity or type of sphingolipid species present inmutant versus wild type adult flies and during various stages ofdevelopment was determined as described below.

Methods were as described in Example 9.

Results: The modified C₁₄S-1-P peak was ten-fold higher in theDrosophila SPL mutant than in the wild type (using an internal standardto normalize for extraction variation), supporting the notion that thephenotype of the SPL mutant may be due to abnormal accumulation ofphosphorylated sphingoid bases and resulting abnormalities in signaling.C₁₄ sphingosine was also increased in the mutant, but to a lesser extent(Table 2). No other peaks in the mutant demonstrated a significantdifference in comparison to wild type controls.

TABLE 2 Sphingolipid Quantification (nmol/200 mg flies) Line (n = 3)modified C₁₄S-1-P C₁₄S Canton S (wild type) 0.49 ± 0.07 2.61 ± 0.27 SPLmutant 4.49 ± 0.53 5.27 ± 0.73

Example 11 Characterization of the SPL Activity Encoded by ESTsLP04413/GH3783 and which is Absent in Insertional Mutant 11393

Drosophila ESTs LP04413 and GH3783 encode a protein with strong homologyto other sphingosine phosphate lyases (SPL). Mutant 11393 whichdemonstrates the flight defect and dorsal longitudinal muscle (DLM)abnormalities described above in Example 7, contains a p-elementinsertion within this locus. Initial results using a standard SPL assayand a radiolabelled C₁₈DHS-1-P substrate indicated that Drosophila ESTsLP04413 and GH3783 encode an SPL, since expression restored SPL activityto a yeast SPL mutant. However, the activity conferred by the ESTexpression in yeast was not pronounced. Since Drosophila extractscontain C₁₄ sphingosine and a modified species of C₁₄S-1-P, it washypothesized that the C₁₈DHS-1-P was not a favorable substrate for themajor Drosophila lyase. Further, residual lyase activity observed in themutant indicated the presence of more than one SPL activity inDrosophila. Therefore, the optimal substrate of the SPL encoded by ESTsLP04413 and GH3783 was determined and this activity was differentiatedfrom other SPL activities in Drosophila.

Methods: Wild type (Canton S) and mutant whole fly extracts wereprepared by mechanical disruption. Standard SPL assays using C₁₈ DHS-1-Psubstrate were performed as previously described (Van Veldhoven, P. P.,and G. P. Mannaerts. 1991. Subcellular localization and membranetopology of sphingosine-1-phosphate lyase in rat liver. J Biol Chem.266:12502-12507). An HPLC-based SPL assay was established, to allow forvarious non-radioactive substrates to be evaluated. For this assay,C₁₄S-1-P, C₁₈DHS-1-P and modified C₁₄S-1-P were prepared by drying downthe lipid extract from 15 mg of 11939 flies, plus 200 pmol C₁₄S-1-Pstandard and 200 pmol C₁₈DHS-1-P standard. Lipids were resuspended in 25μl of 1% Triton X-100 in potassium phosphate buffer, pH 7.4. 175 μl ofreaction buffer (KP buffer, NaF, DTT, EDTA, sucrose) were added, andmixture was tip sonicated for 20 seconds, followed by addition of 50 μgof protein from whole cell extract of flies (CS or 11939) or Δdpl1:lcb4yeast overexpressing the fly lyase. Incubation proceeded for 1 hr at 37°C. Reaction was stopped by adding 175 μl of MeOH containing 0.2% aceticacid. The reaction was applied to STRATA C18 column in 40% MeOHcontaining 0.1% acetic acid. The column was washed with 600 μl of 40%MeOH containing 0.1% acetic acid. Lipids were eluted with 1 ml of 90%MeOH/10% 10 mM K-Phosphate, pH 7.2. Samples were dried and resuspendedin MeOH, treated with o-pthalaldehyde and injected on the HPLC. Thedegradation of S-1-P standards and modified C₁₄S-1-P were compared tostandards incubated in the absence of protein extracts.

Results: An activity which metabolizes modified C₁₄S-1-P is present inwild type fly extracts but is absent in the mutant fly extracts.Residual SPL activity does exist in the mutant fly. This activity isdistinct from that encoded by LP04413/GH3783, in that it metabolizesC₁₄S-1-P and C₁₈DHS-1-P with an efficacy similar to or better than wildtype. The pH curve of the residual SPL activity in mutant flies isidentical to that seen in wild type flies (against a C₁₈DHS-1-Psubstrate), indicating that this activity is not disrupted in themutant.

Example 12 Further Characterization of the Drosophila melanogaster SPLMutant Phenotype

Adult SPL mutant flies demonstrated inability to fly and abnormalpatterning of indirect flight muscles. The adult SPL mutant fliesconsistently demonstrated abnormal patterning of DLMs, although thenumber of remaining DLMs varied in each mutant. In this Example, it wasdetermined whether the abnormal muscle development was limited to theadult fly, or whether the defect was also present at earlierdevelopmental stages.

Methods: Larval locomotor assay. Third instar larvae were placed on aclear agar substrate that overlays a grid. A light source at one endprovided a photactic stimulus. Distance traveled was scored during threeminute trials. Larval muscle microscopy. Larvae were filleted during thethird instar and pinned with the dorsal cuticle down. The viscera wereremoved to allow an unobstructed view of the body wall muscles usingpolarized light. Muscles were refractile due to the presence offilamentous arrays in each muscle fiber.

Results: 11393 mutant larvae demonstrated significant defects inlocomotion in comparison to wild type larvae, although phototacticresponse is intact. In all mutant larvae examined, the T2-dorsal obliquemuscles exhibited alterations in number and/or size. Fused,hypertrophied residual dorsal obliques were observed in the mutants.

Since the four pairs of dorsal obliques in thoracic segment two createscaffolds which give rise during pupation to the DLM structures of theadult, it is likely that the developmental defect seen in the adult isthe result of a process which begins much earlier, during larvaldevelopment or embryogenesis.

Example 13 Human SPL Expression Patterns in Cancer

To determine if SPL expression is altered in human tumors, we utilized acancer profiling array which contains more than 240 cDNA pairsrepresenting tumor tissue and corresponding normal tissue from the samepatient. By utilizing tissue pairs from one patient, differences betweengene expression in tumor and normal tissue which might be due to personto person variability should not confound the interpretation of results.Additionally, each blot was normalized for loading using four separatehousekeeping genes. Traditional hybridization techniques were utilizedto probe this cDNA blot with a 300 nucleotide 3′ fragment of human SPLcDNA (SEQ ID NO:7), which was obtained from the previously describedcloning experiments. Analysis of the array indicated that, whereas humanSPL expression is matched closely in most tissue pairs, it issignificantly reduced in colon cancer specimens, with a 50% reduction inexpression in colloid cancer of the colon and 61% reduction inadenocarcinoma of the colon. Reduced SPL expression was also seen inadenocarcinoma of the uterus. None of the tumors in which SPL expressionis diminished demonstrate SK overexpression. Thus, altered SPLexpression is observed in primary human tumors. Therefore, modulatingthe activity of SPL protein either by altering gene expression orthrough direct action on the protein may provide a useful treatment forindividuals afflicted with an SPL-related cancer. Furthermore, SPLexpression serves as a useful diagnostic marker of cancer in humans.

All of the above U.S. patents, U.S. patent application publications,U.S. patent applications, foreign patents, foreign patent applicationsand non-patent publications referred to in this specification and/orlisted in the Application Data Sheet, are incorporated herein byreference, in their entirety.

From the foregoing it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims.

1. An isolated antibody that binds to a polypeptide selected from thegroup consisting of: (a) a polypeptide comprising the sequence recitedin SEQ ID NO:8, or a fragment thereof; (b) a polypeptide comprising anamino acid sequence encoded by a polynucleotide comprising apolynucleotide selected from the group consisting of: i. the sequencerecited in SEQ ID NO:7; and ii. nucleotide sequences isolated from humanthat hybridize to a polynucleotide complementary to SEQ ID NO:7 undermoderately stringent conditions, wherein said conditions compriseprewashing in a solution of 5×SSC, 0.5% SDS, 1.0 mM EDTA (pH 3.0);hybridizing at 50-65° C., 5×SSC, overnight; followed by washing twice at65° C. for 20 minutes with each of 2×, 0.5× and 0.2×SSC containing 0.1%SDS, and wherein the nucleotide sequences encode polypeptides havingsphingosine-1-phosphate lyase activity.
 2. The antibody of claim 1,wherein the antibody is a monoclonal antibody.
 3. An antibody accordingto claim 1 or claim 2, wherein the antibody inhibits the ability of apolypeptide having a sequence recited in SEQ ID NO:8 to degradesphingosine-1-phosphate.
 4. A method for detectingsphingosine-1-phosphate lyase in a sample, comprising: (a) contacting asample with an antibody according to claim 1 or claim 2 under conditionsand for a time sufficient to allow the antibody to bind tosphingosine-1-phosphate lyase; and (b) detecting in the sample thepresence of sphingosine-1-phosphate lyase bound to the antibody.
 5. Akit for detecting sphingosine-1-phosphate lyase in a sample, comprisingan antibody according to claim 1 or claim 2 and a buffer or detectionreagent.